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Microfabrication technology has made a considerable impact on recent biotechnological research. The area-selective integration of self-assembled monolayer (SAM) on patterned substrates is important to biosensor fabrications, cell studies, and tissue engineering applications. The combination of them will be an interesting field for many kinds of applications. In this work, synchrotron radiation (SR) stimulated etching was conducted to make the micro-pattern of SiO/sub 2/ thin film with a Co contact mask and the dodecene SAM was deposited on the etched surface area-selectively. From the experimental results, we conclude that Co is suitable to the mask materials in the SR etching, and that the exhibiting patterning technique is suitable for the area-selective deposition of alkyl SAMs.